Anyone who has used a Logitech Harmony remote knows that while the programming interface is simple, it's no small task to get the remote configured 'just right'. You can fully expect to be in the application a lot for the first few weeks, always mapping a button, or tweaking an 'activity'. Making the remote control a PC is quite a bit more of a headache than I expected, but the end results are quite satisfying.
What you need to make this happen is a bit confusing, as the Logitech Harmony series of remotes are not 'Universal Remotes' so much as they are 'Remote Aggregators'. Chances are unless you've used a Harmony, you're wondering what a 'Remote Aggregator' is. Honestly, I just made it up, but it fits.
With a normal universal remote, you provide some Manufacturer's codes and in a few minutes you're able to power on your DVD player, cable box, and TV within a few seconds of each other.
Harmony remotes work a little differently. It's an "activity" based remote, which means you set up "Activities" (duh) involving multiple pieces of equipment using Logitech's programming interface. Usually you can just tell it the make and model of the device you wish the remote to replicate, and away it goes.
Unfortunately, even though Logitech is a company that is almost entirely based around PC peripherals, you cannot just punch in "Windows Computer" and watch it blow your mind. You have to make it replicate an existing Windows remote. Doing this is not time efficient, but is not too painful.
1) Acquire a PC remote control (yes, you must actually buy a remote to make your Harmony remote work). This is why the $9 DealExtreme remote stands out as such a good deal; you need both a USB IR Receiver, and a Remote to copy commands from. The remote is junk from a quality standpoint, but has a number of nice features, requires zero configuration to work on most computers, and being you only need to use it for maybe an hour, has a nice pricetag. You should be able to use the following guide for ANY remote to teach the Harmony, but an official MCE remote would take the least amount of work (I think, anyway).
2) Wait for the remote to be delivered. Once it shows up, continue on to part 2!